Hello,
I've spent some time lurking here on the site and have not seen this combination mentioned.
I have a Sky3DS, so that I can back-up and move my save files to my PC. What I get is a .SAV file.
I have tried deleting and re-instating the .SAV file - and it seemed to work without a problem, placing me in the right place with the right pokemon. My guess is that it means I have apparently all the necessary data in the .SAV file.
How can I then extract/convert the .SAV, so that I can use it in the PKHEX and modify it?